Relative Performance of All Tested Motif Alignment Strategies

Performance is measured as the percent of motifs whose structural class are correctly recovered via the best hit in database searches. The two datasets used in this comparison are taken from JASPAR and TRANSFAC. While accuracy was measured over the complete dataset, the results below report separately the performance for the nonzinc-finger families (non-ZNF; ten families in JASPAR, 20 in TRANSFAC) and the zinc-finger families (ZNF; three in JASPAR, five in TRANSFAC). Average is the weighted average. Overlapping (overlap) and ungapped (ungapped) alignments are specified. Gap extension is equal to half the gap opening. (243 KB DOC)